Genetic Structure and Diversity in Oryza sativa L

Garris et al. Page 1

Genetic structure and diversity in Oryza sativa L.

Amanda J. Garris*1, Thomas H. Tai†2 , Jason Coburn*, Steve Kresovich*, and Susan McCouch*

*Plant Breeding Dept, Cornell University, Ithaca, NY 14853-1901

†USDA-ARS Dale Bumpers National Rice Research Center, Stuttgart, AR 72160

1 Present address: USDA-ARS Plant Genetic Resources Unit, Geneva, NY 14456

2 Present address: USDA-ARS Crops Pathology and Genetics Research, Agronomy and Range

Science, University of California, Davis, CA 95616

Genetics: Published Articles Ahead of Print, published on January 16, 2005 as 10.1534/genetics.104.035642


Running head: Genetic structure and diversity

Keywords: rice, population genetics, diversity

Corresponding author: Susan McCouch 162 Emerson Hall Cornell University, Ithaca, NY 14853 Email: [email protected] Phone: 1(607) 255-0420 Fax: 1(607) 255-6683


ABSTRACT

The population structure of domesticated species is influenced by the natural history of the

populations of pre-domesticated ancestors, as well as by the breeding system and complexity of

the breeding practices exercised by humans. Within Oryza sativa, there is an ancient and well-

established divergence between the two major sub-species, indica and japonica, but finer levels

of genetic structure are suggested by the breeding history. In this study, a sample of 234

accessions of rice was genotyped at 169 nuclear SSRs and two chloroplast loci. The data were

analyzed to resolve the genetic structure and to interpret the evolutionary relationships between

groups. Five distinct groups were detected, corresponding to indica, aus, aromatic, temperate

japonica and tropical japonica rices. Nuclear and chloroplast data support a closer evolutionary

relationship between the indica and aus, and between the tropical japonica, temperate japonica

and aromatic groups. Group differences can be explained through contrasting demographic

histories. With the availability of rice genome sequence, coupled with a large collection of

publicly available genetic resources, it is of interest to develop a population-based framework for

the molecular analysis of diversity in O. sativa.


INTRODUCTION

Asian cultivated rice (Oryza sativa L.) holds a unique position among domesticated crop species

in that it is both a critical food staple and the first fully sequenced crop genome. Rice is

consumed as a grain almost exclusively by humans, supplying 20% of daily calories for the

world population (World Rice Statistics, http://www.irri.org; FAOSTAT, http://apps.fao.org). As

a model organism with a fully sequenced genome, rice affords unique opportunities to use

genomic approaches to study its domestication, adaptive diversity, and the history of crop

improvement.

Archeological evidence supports a similar time of domestication for rice, wheat (Triticum

aestivum) and maize (Zea mays ssp mays), 5 - 10,000 years ago, but the evolutionary histories of

these cereals differ in several significant ways (PIPERNO and FLANNERY 2001; SHARMA and

MANDA 1980; SOLHEIM 1972; ZOHARY and HOPF 2000). Recent studies tracing the molecular

evolution of maize offer several points of comparison that help illuminate the genetic history of

rice. Unlike maize, rice is predominantly autogamous and hence, gene flow is restricted. As a

result, geographically or ecologically distinct groups of rice are expected to show greater genetic

differentiation than would be the case in an outcrossing species. Because of fewer opportunities

for cross-pollination, the structure of landraces in rice and maize is also predicted to be

fundamentally different. A greater proportion of diversity is expected to reside in differences

between homozygous lines within a heterogenous landrace in rice (OLUFOWOTE et al. 1997)

compared to the distribution of diversity among heterozygous individuals within a landrace of

maize (LABATE et al. 2003). In addition, evidence suggests that the two primary sub-species of

rice, indica and japonica, are the products of separate domestication events from the ancestral


species, Oryza rufipogon, a hypothesis initially based on studies of biochemical traits (SECOND

1982) and hybrid sterility (KATO et al. 1928), and subsequently supported by molecular analyses

(CHENG et al. 2003; DOI et al. 2002). This is in contrast to the single domestication event that led

to the evolution of modern maize (MATSUOKA et al. 2002).

At all levels of analysis, the differences between the indica and japonica sub-species are very

apparent. Differences between non-sticky (indica) and sticky (japonica) rices are documented in

Chinese literature as early as 100 AD (MATSUO 1997). In eco-geographical terms, indica are

primarily known as lowland rices that are grown throughout tropical Asia, while japonica are

typically found in temperate East Asia, upland areas of Southeast Asia and high elevations in

South Asia. The traits that have been used to classify indica and japonica have included grain

shape, phenol reaction, sensitivity to potassium chlorate, leaf color and apiculus hair length,

though the spectra of variation for any of these individual traits overlap in the two subspecies

(OKA 1988).

Using RFLPs, the indica-japonica division was very clear (NAKANO et al. 1992; WANG and

TANKSLEY 1989; ZHANG et al. 1992) but additional population structure consisting of the six

varietal groups indica, japonica, aus, aromatic, rayada, and ashina was discerned using 15

isozyme loci (GLASZMANN 1987). The aus, rayada, and ashina are minor groups that have

generally been considered to be ssp. indica ecotypes, and all have a comparatively small

geographic distribution along the Himalayan foothills. The drought-tolerant, early maturing aus

rices are grown in Bangladesh during the summer season from March to June. Rayada and

ashina are floating rices of Bangladesh and India, respectively. Aromatic rices such as basmati


from Pakistan, Nepal, and India and sadri from Iran have a distinctive popcorn-like aroma and

are highly prized for their quality. Because there has been no reliable way to distinguish ecotypes

based on phenotypic evaluation, and because information about the varietal groupings is rarely

available from genetic resource collections, a genetically-based identification of groups is

required to fully utilize these resources.

The purpose of this study is 1) to establish a population genetics framework for the evaluation of

rice by characterizing the intraspecific divergence within a set of 234 rice accessions using

simple sequence repeats (SSR) and chloroplast sequence, and 2) to address the evolutionary

relationships among groups within the species. Intraspecific classification of rice has been of

importance to rice geneticists and breeders, but with the advent of population genetics

approaches, it is now feasible to examine the genetic basis of domestication, adaptation, plant

development and agricultural performance. Simple sequence repeat (SSR) loci are particularly

useful for the study of population structure and demographic history of domesticated species

because their high level of allelic diversity facilitates the detection of the fine structure of

diversity more efficiently than an equal number of RFLP, AFLP or SNP loci. The specific goals

of this study are to characterize population structure within Oryza sativa, to examine the

differences between, and relationships among, genetically-defined groups and to analyze aspects

of demographic history that may explain them. The resulting framework will be used to pose

questions about the origin and diversity of genepools that exist within cultivated Asian rice and

to lay the foundation for characterizing the genes that distinguish them.


MATERIALS AND METHODS

Plant material

We sampled 234 rice accessions representing the geographic range of Oryza sativa. The sample

included accessions collected in Asia (187), the Americas (27), Africa (14), Europe (3), and

Oceania (2). Information about the accessions used (accession name, accession number, seed

source, country of origin, membership in one of the five model-based populations, accession

number cited in Supplemental Figure S1, and choloroplast haplotype) is listed in supplemental

Table S1 at http://www.genetics.org/supplemental/. Aroma of rice leaves was evaluated using the

protocol of PINSON (1994), modified to include warming the samples in a 67ºC water bath for 10

minutes prior to analysis.

Genomic DNA extraction and SSR genotyping

DNA was extracted using a modified potassium acetate-SDS protocol (DELLAPORTA et al. 1983).

The 169 nuclear SSRs employed to analyze population structure is published in supplemental

Table S2 as supporting information on http://www.genetics.org/supplemental/ (CHEN et al. 1997;

COBURN et al. 2002; TEMNYKH et al. 2001; TEMNYKH et al. 2000). PCR was performed as in

Coburn et al. (2002) except that mixtures contained 20 ng template DNA, 4 pmols of forward

and reverse primers, and 1 unit of Taq polymerase. Pooled PCR products, diluted to equalize

signal strength, were size separated by capillary electrophoresis using an ABI Prism 3700 DNA

Analyzer (Applied Biosystems, Foster City, CA). SSRs were analyzed with GenScan 3.1.2

software (Applied Biosystems) and scored with Genotyper 2.5 software (Applied Biosystems).

Genotype data for all accessions is available at

http://ricelab.plbr.cornell.edu/publications/2004/garris/Genotype_Data/.


Chloroplast sequencing

The plastid subtype-identity (PS-ID) sequence, which captures linker sequences between plastid

genes rp116 and rp114, was amplified as reported by (NAKAMURA et al. 1998). A second

fragment, ORF100, is known to harbor length variation in rice, and was amplified as in

Nakamura (1998), except that a new forward primer was designed to amplify a smaller fragment

(5’CAACCCACCCCATAAAATTG 3’). 10 µl of quantified PCR product was treated with 10

units Exonuclease I and two units shrimp alkaline phosphatase and incubated at 37ºC for 15

minutes followed by 80ºC for 15 minutes. Single pass sequencing was performed by automated

sequencing using an ABI Prism 3700 DNA Analyzer (Applied Biosystems, Foster City, CA) at

the Cornell BioResource Center (Ithaca, NY). Direct sequencing of PCR products resulted in a

homozygous sequence. Sequences were aligned using Sequencher 4.0.5 (Gene Codes, Inc., Ann

Arbor, MI) for base calling and CLUSTAL W (THOMPSON et al. 1994) with manual quality

control for insertion/deletions. The ends of fragments were trimmed to remove low quality

sequence.

Statistical Analysis

Genetic distance was calculated using the C.S. Chord distance (CAVALLI-SFORZA and EDWARDS

1967) because it has been shown by analysis of simulations to generate correct tree topologies

regardless of the microsatellite mutation model (TAKEZAKI and NEI 1996). Phylogenetic

reconstruction was based on the neighbor-joining method implemented in PowerMarker version

2.7 (LIU and MUSE 2004; http://www.powermarker.net) In addition, the model-based program

STRUCTURE (FALUSH et al. 2003; PRITCHARD et al. 2000) was used to infer population


structure using a burn-in of 10,000, run length of 100,000, and a model allowing for admixture

and correlated allele frequencies. Five independent runs yielded consistent results. Inferred

ancestry for each accession and the key for identifying the accessions shown in the Neighbor-

Joining tree is available as supporting information on the Genetics website as supporting Table

S1 and supporting Figure S1. The graphical display of the STRUCTURE results was generated

using Distruct software (ROSENBERG 2002, http://www.cmb.usc.edu/~noahr/distruct.html).

PowerMarker was used to calculate the average number of alleles, gene diversity, and

Polymorphism Information Content (PIC) values. FST, the correlation of alleles within

subpopulations, was calculated using an AMOVA approach in Arlequin V2.000 (SCHNEIDER and

EXCOFFIER 1999; WEIR 1996). In order to utilize analysis approaches which are based on the

Stepwise Mutation Model (SMM), a set of 60 SSR loci that behaved in a stepwise manner (fewer

than 10% of alleles were at non-stepwise intervals) was identified (as indicated in the list of

SSRs published supplemental Table S2 which is published as supporting information on the

Genetics web site). This set of loci was used for analysis of directional evolution and population

bottlenecks. Average standardized allele sizes for analysis of directional evolution were

calculated as in VIGOUROUX et al. (2003). Ascertainment bias was assessed by comparing the

difference in allele lengths between ssp. indica and japonica when the markers were originally

derived from cv. IR36 (indica, 67 markers), or cv. Nipponbare (japonica, 100 markers).

Ascertainment bias was non-significant (t = 0.24, p-value = 0.83).

The program BOTTLENECK (CORNUET and LUIKART 1996) was used to test each group for

deviation from mutation-drift equilibrium under the Stepwise Mutation Model (SMM). This

program conducts test for recent (within the past 2Ne to 4Ne generations) population bottlenecks


that severely reduce effective population size (Ne) and produce an excess in heterozygosity.

Significance was determined by the sign, standardized differences and Wilcoxon tests.

RESULTS

Genetic structure in rice

Analysis of genetic distance and population structure provided evidence for significant

population structure in rice. Analysis of these data, using STRUCTURE, produced the highest

log likelihood scores when the number of populations was set at five, which was consistent with

clustering based on genetic distance. Most accessions were classified into one of the five groups,

which corresponded to indica (79), aus (20), aromatic (19), temperate japonica (45), and

tropical japonica (44) (Figure 1). In addition to the accessions that were clearly assigned to a

single population, where greater than 80% of their inferred ancestry derived from one of the

model-based populations, 24 accessions (10%) in the sample were categorized as having

admixed ancestry (Figure 2). While the majority of these were identified as admixture between

temperate and tropical japonica groups, other admixture combinations were present as well

(Figure 2; Supplemental Table S1).

The overall AMOVA indicates that 37.5% of the variation was due to differences among groups

with the remaining 62.5% due to differences within groups. Pairwise estimates of FST using the

AMOVA approach indicated a high degree of differentiation between the five model-based

groups with values ranging from 0.20 to 0.42 (Table 1). Lower levels of differentiation were

observed in pairwise comparisons of temperate with tropical japonica (0.20) and aus with indica

(0.25).


Chloroplast diversity

As an alternative method to assess the relationships among populations, two plastid loci were

examined. Overall, there were eight chloroplast haplotypes based on five polymorphic sites (two

indels, one SNP, and a polyC/polyA region) in the PSID and ORF100 fragments (Supplemental

Table S1 and Figure 1). The indica subpopulation contained the most chloroplast diversity,

harboring seven of the eight haplotypes and encompassing all the chloroplast diversity found in

the temperate and tropical japonica groups. Four of the eight haplotypes were observed in aus

chloroplasts, and these represented the most frequent indica haplotype as well as one found in

higher frequency in the japonicas. Only two haplotypes were found in the japonica sub-

populations and both were shared between the temperate and tropical groups. The aromatic rices

share a more recent maternal ancestor with the japonica, consistent with their position based on

nuclear SSRs, but 15% of aromatic rices also contained a 4 bp deletion in the ORF100 fragment

that was unique to this group.

Nuclear diversity

The amount and organization of genetic diversity differed among the model-based populations

(Table 2). The indica and tropical japonica groups contained a high percentage of polymorphic

loci (99%), and an average of 7.26 and 6.09 alleles per locus, respectively. Even with a much

smaller sample size, the aus group had very high diversity with 98% of loci polymorphic and an

average of 5.1 alleles per locus. These three groups also had the highest heterozygosity values

(0.55 for indica, 0.54 for aus, 0.47 for tropical japonica). The temperate japonica and aromatic

groups had lower diversity with 91% and 88% polymorphic loci and 4.9 and 3.4 alleles per


locus, respectively, and lower HE values, (0.39 for both temperate japonica and aromatic). The

temperate japonica and aromatic populations also had the highest incidence of monomorphism,

with 15 and 21 monomorphic loci, respectively. Interestingly, the alleles at all 15 monomorphic

loci in the temperate japonica group were identical in size to the most frequent allele among the

tropical japonica. This observation is consistent with the hypothesis that temperate japonica

rices were derived from tropical japonica. For 15 of the 21 monomorphic loci in the aromatic

sample, the allele was identical in size to the most frequent allele in the tropical japonica, and

this was often the most frequent or only allele in the temperate japonica.

Directional evolution in allele length

It has been proposed that there is an upwards bias in the number of repeats responsible for the

hypervariability of SSRs which would lead to larger average allele sizes in “derived” groups

(RUBINSZTEIN et al. 1995). This has been shown to be true in the comparison of humans and

non-human primates (RUBINSZTEIN et al. 1995) and in non-ancestral populations of maize

(VIGOUROUX et al. 2003). Using the framework established by the population structure analysis,

comparisons of allele lengths between groups using the subset of 60 SSR loci that have evolved

in a stepwise fashion resulted in statistically significant differences among some populations of

rice (Table 3). The average standardized allele lengths in the indica, aus and aromatic groups

were significantly smaller than those in the temperate and tropical japonica groups though the

allele lengths in the indica, aus, and aromatic groups were not statistically different from each

other. Furthermore, in the comparison between temperate and tropical japonica, the average

standardized allele size is greater in the former (t = 9.31, p < 0.0001), supporting the hypothesis

that the temperate japonica group is derived from the tropical japonica group.


Population bottlenecks

The observed differences in diversity among the rice populations suggest differences in

demographic history that have shaped these patterns. In order to assess the effect of historical

population sizes in the distribution of diversity, we examined the five model-based populations

for evidence of recent bottlenecks. A likely cause of differences in the effective population sizes

of the rice groups is the proximity, duration, and severity of population bottlenecks. Deviation of

allelic diversity and heterozygosity from mutation-drift equilibrium under the Stepwise Mutation

Model (SMM) was assessed to determine whether any of the genetic populations had recently

experienced a bottleneck. Analysis of a set of 60 di-nucleotide SSR markers that exhibited

stepwise mutation patterns revealed strong evidence of bottlenecks for the aus, aromatic,

temperate japonica and tropical japonica populations. These data did not support a recent

bottleneck in the indica population. There is currently no available estimate for the mutation rate

of SSRs in rice, which would assist in the estimation of the time since the divergence of these

groups.

DISCUSSION

Genetic structure has been previously documented in rice (GLASZMANN 1987; NI et al. 2002;

PARSONS et al. 1999), but this analysis combines a large number of accessions (234) with a large

number of loci (169). The O. sativa rice accessions sampled show significant differentiation into

five groups: aromatic, aus, indica, temperate japonica, and tropical japonica. This deep genetic

structure is, in part, a legacy of structure in ancestral rice populations. Analysis of sequence

divergence between cv. GLA4, an indica cultivar and cv. Nipponbare, a temperate japonica,


suggests that these two groups diverged approximately 440, 000 years ago, supporting the

hypothesis that indicas and japonicas are derived from independent domestication events from

an ancestral rice which had already differentiated into (at least) two gene pools (CAI and

MORISHIMA 2002; MA and BENNETZEN 2004; YAMANAKA et al. 2004). Sequence divergence

between the chloroplast genomes of cv. 93-11, an indica, and cv. PA64S, an indica-like variety

with a japonica chloroplast, yielded a divergence time of 86,000-200,000 years ago (TANG et al.

2004). These results suggest that the divergence between indica and japonica in our sample is in

part due to differentiation of ancestral O. rufipogon populations in different locations and at

different times. Rice presents a contrast to the history of domestication of maize, which involved

a single domestication event with a clear geographic center and expansion to the north and south

(MATSUOKA et al. 2002). As sequence comparisons in rice are enlarged to include

representatives of each subpopulation, the relationships among the groups can be clarified and

the times of divergence estimated.

The deep genetic structure in rice may also be an effect of the autogamous breeding system. In

self-pollinated species, one would predict a greater partitioning of diversity among rather than

within populations in the absence of human mediated gene flow between populations by

breeding. Indeed, the large amount of variation attributable to differences between groups in rice

(37.5% in this study) can be compared to results of a comparable sample of maize inbred lines,

in which only 8.3% of the variation was due to differences between groups (LIU et al. 2003).

While both breeding system and domestication history have had large effects on the structuring

of diversity in rice, the independent population histories of the groups have also shaped the


genepools. For example, the indica is a diverse group relative to the others with no evidence of a

genetic bottleneck. The source of this variation could include mitigation of the domestication

bottleneck by gene flow with sympatric wild relatives or a historically larger effective population

size due to overland dispersal routes.

The aus had high diversity values relative to its sample size and, like the indica, contained

several chloroplast haplotypes. Aus rices were traditionally grown in a short summer season in

Bangladesh under rainfed conditions (PARSONS et al. 1999). Adaptation to flowering under long

days required evolution of day length neutrality, fostering temporal reproductive isolation and

divergence. Although the aus types have a historically smaller geographical distribution and

receive less attention than indica and japonica rices in breeding programs, their drought

tolerance and early maturity are adaptive traits that could be usefully targeted in breeding

applications.

The temperate and tropical japonica have a very close genetic relationship and have overall

lower genetic diversity than the indica (GLASZMANN 1987; NI et al. 2002; ZHANG et al. 1992) as

well as larger standardized allele lengths. In contrast to indica, which was able to utilize land

routes for migration, many of the tropical japonicas in our sample were collected from the

islands of Indonesia and the Philippines where migration via islands could have acted to decrease

diversity by a chain of bottlenecks. In addition, the two japonica groups represent an adaptive

spectrum of an ancient sub-population from tropical origins to temperate latitudes, with the

necessary adaptations to environmental signals such as day length and temperature. As the only

pair-wise comparison that embodies such obvious adaptation to a new environment, the


temperate and tropical japonica groups offer a valuable tool for studying the genetic basis of

adaptation. The statistical significance of the larger allele size in the temperate relative to the

tropical japonica group supports the hypothesis that temperate japonica were derived from the

tropical japonica group. One explanation for the differences in average allele lengths is a higher

mutation rate in the temperate population. Previous observations of enhanced transposable

element activity in temperate compared to tropical japonica groups (JIANG et al. 2002) suggest

that this hypothesis may be worthy of further investigation.

Previously described as intermediate between indica and japonica rice (AHUJA et al. 1995),

aromatic rice forms a distinct sub-group in this and other studies (JAIN 2004). Both the nuclear

and chloroplast data demonstrate a close relationship to the japonicas. The aromatic group had a

high proportion of monomorphic loci suggestive of a severe or recent bottleneck (NAGARAJU et

al. (2002), and this study). The genetics of aroma may contribute to the apparent genetic

bottleneck in this group (GARLAND et al. 2000; LORIEUX et al. 1996) but this question awaits

further research.

In addition to the groups identified by this analysis, ten percent of individuals show evidence of

mixed population ancestry. In some cases these admixed individuals are likely to be the result of

modern breeding, in other cases they may be landraces belonging to groups that were

underrepresented in our sample. For example, Ashina and rayada rices (isozyme-based varietal

groups III and IV) comprised only 1% of all 1688 varieties sampled by Glaszmann (1987), and

their adaptation to deep water conditions makes them less amenable to ex situ conservation. The

identities of some admixed individuals could perhaps be better resolved through deliberate


addition of deepwater rices to the dataset. The public availability of the genotypic data presented

here should facilitate further characterization of rice population structure and diversity and

highlights the need for research complementary research on the regional and national levels.

Using this framework of genetically defined populations, it may be possible to exploit the rice

gene pools more effectively with population genetics-based approaches using the extensive

collections of rice genetic resources. In particular, different subpopulations are likely to provide

differing levels of resolution for association mapping studies (GARRIS et al, 2003) as well as

different allele frequencies associated with desirable traits for plant improvement. In an

evolutionary context, many of the most intriguing questions remain to be answered, such as to

what extent allelic distribution in O. sativa is shaped by these populations, whether a pre-

domestication divergence between indica and japonica can be detected in O. rufipogon and O.

nivara ancestral groups, and whether comparisons among populations will help identify loci

showing footprints of selection. Studies designed to address these and other questions will lead

to a better understanding of the processes of domestication and adaptation in this cultivated,

inbreeding species.

ACKNOWLEDGEMENTS

We wish to thank D. Mackill of the International Rice Research Institute in the Philippines, H.

Bockelman of the National Small Grains Collection in Aberdeen, Idaho, R. Dilday and J.N.

Rutger of the Dale Bumpers National Rice Research Center and K. Moldenhauer of the Rice

Research and Extension Center in Stuttgart, Arkansas for seeds, E. Septiningsih for developing

the RM623 primer pair, S. Harrington for editing spellings and checking accession numbers in


Supplemental Table 1 and L. Swales for formatting. We also thank J. Edwards and E. Buckler

for critical reading of the manuscript prior to submission. This research was supported by USDA

NRICGP No. 00-35300-9216 (T.H.T. and S.R.M.) and CRIS Project 6225-21000-006 (T.H.T.).

A.J.G. was supported by USDA/CSRS Competitive Grant 97-35300-5101, representing Food

and Agricultural Sciences National Needs Graduate Fellowship in Plant Biotechnology.


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Figure Legends

Figure 1. Unrooted Neighbor-joining (NJ) tree based on C.S. Chord (Cavalli-Sforza and

Edwards, 1967) based on 169 nuclear SSRs. The key to the left relates the color of the line to the

chloroplast haplotype based on ORF100 and PS-ID sequences. Admixed individuals are

identified with an asterisk (*). Bootstrap values (out of 100) for indica, aromatic, and aus are

indicated at the branch points.

Figure 2. Model-based ancestry for each accession. Color codes are as follows: aromatic

(purple), aus (orange), indica (yellow), temperate japonica (dark blue), and tropical japonica

(light blue).

Supplemental Figure S1. Unrooted Neighbor-joining (NJ) tree based on C.S. Chord (Cavalli-

Sforza and Edwards, 1967) based on 169 nuclear SSRs. The key to the left relates the color of

the line to the chloroplast haplotype based on ORF100 and PS-ID sequences. Admixed

individuals are identified with an asterisk (*). Supplemental Table S1, published as supporting

information on the Genetics web site, provides a key to accession identities.


Table 1. Pairwise FST values and AMOVA.*

Aromatic Aus Indica Temp. Jap. Trop. Jap.

Aromatic 0.34 0.39 0.37 0.31

Aus 0.28 0.26 0.44 0.37

Indica 0.34 0.25 0.45 0.39

Temp. Jap 0.29 0.42 0.43 0.22

Trop. Jap. 0.23 0.35 0.36 0.20

*AMOVA-based estimates appear above the grey diagonal and classical

estimates (θ) appear below the diagonal. For AMOVA-based estimates,

p< 0.000001 for 110 permutations for all population comparisons.


Table 2. Summary of polymorphism for total dataset and by population.

Standard deviations are indicated in parentheses.

All Aus Indica Aromatic Temp. Jap. Trop. Jap.

Sample size 234* (7.35) 21 (0.990) 79 (2.92) 19 (1.85) 41 (2.24) 48 (1.73)

Avg. no. of

alleles/locus 11.8 (7.35) 5.1 (2.73) 7.3 (4.44) 3.4 (2.00) 4.9 (3.68) 6.1 (3.90)

Avg. gene diversity 0.7 (0.16) 0.54 (0.23) 0.55 (0.24) 0.39 (0.26) 0.39 (0.28) 0.47 (0.27)

Avg. PIC value 0.67 (0.18) 0.52 (0.22) 0.52 (0.24) 0.38 (0.24) 0.37 (0.27) 0.46 (0.26)

*Includes admixed


Table 3. Differences in average standardized allele sizes for pairs of populations.

Aromatic Aus Indica Temp. Jap. Trop. Jap.

Aromatic 1.1824NS 1.0143NS 13.1320* 6.3997*

Aus 0.4801NS 11.4668* 6.6454*

Indica 6.2148* 4.0691*

Temp. Jap. 9.3128*

Trop. Jap.

NSnot significant (p>0.05)

*p<0.0001

Genetic Structure and Diversity in Oryza sativa L

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